def do_process(args):
"""Process arguments of the script
"""
if args.filename:
fname = args.filename[0]
print("Processing file: ", fname)
try:
INP = qr.Input(fname)
code = tasks(INP.tasks, INP)
except:
print(traceback.format_exc())
return
if args.output:
print("Script saved as: ", args.output)
else:
print("\nResulting code:\n")
print(code)
def do_command_run(args):
"""Runs a script
"""
m = qr.Manager().log_conf
dc = qr.Manager().get_DistributedConfiguration()
#
# analyzing --verbosity option
#
verb = args.verbosity
try:
vrbint = int(verb)
m.verbosity = vrbint
m.fverbosity = vrbint + 2
except:
try:
vrbint = verb.split(",")
m.verbosity = int(vrbint[0])
m.fverbosity = int(vrbint[1])
except:
raise Exception(
"Integer or two comma separated integers required" +
" for -y/--verbosity option")
# we set the verbosity lower for other than the leading process
if dc.rank != 0:
m.verbosity -= 2
m.fverbosity -= 2
#
# log into file
#
m.log_to_file = args.logtofile
if m.log_to_file:
m.log_file_name = args.filename
#
# parallel options
#
nprocesses = args.nprocesses
flag_parallel = args.parallel
hostfile = ""
if len(args.hostfile) > 0:
hostfile = args.hostfile
#
# some other logging option
#
flag_silent = args.silent
flag_quiet = args.quiet
if args.silent:
m.verbosity = 0
#
# Run benchmark
#
if args.benchmark > 0:
import time
qr.printlog("Running benchmark no. ",
args.benchmark,
verbose=True,
loglevel=1)
import quantarhei.benchmarks.bm_001 as bm
t1 = time.time()
bm.main()
t2 = time.time()
qr.printlog("... done in", t2 - t1, "sec", verbose=True, loglevel=1)
return
#
# Script name
#
if args.script:
scr = args.script[0]
#
# if the file is yaml, look into it to find the script file name
#
# get the file extension
extsplt = os.path.splitext(scr)
ext = extsplt[1]
#
# Reading configuration file
#
# yaml
if ext in [".yaml", ".yml"]:
INP = qr.Input(scr)
# see if the script name is specified, if not use the conf name + .py
try:
script = INP.script
except:
script = extsplt[0] + ".py"
# see if path is defined, if not use local directory
try:
spath = INP.path
except:
spath = "."
scr = os.path.join(spath, script)
#
# Greeting
#
if not flag_quiet:
qr.printlog("", verbose=True, loglevel=qr.LOG_URGENT)
qr.printlog("Running Quantarhei (python) script file: ",
scr,
verbose=True,
loglevel=qr.LOG_URGENT)
#
# Run serial or parallel
#
if flag_parallel:
#
# If this is set to True, we use one more processes than processor
# number to steer other processes
#
# Also set the corresponding flag in the parallel module
#
use_steerer = False
if use_steerer:
nsteerer = 1
else:
nsteerer = 0
#
# get parallel configuration
#
cpu_count = 0
try:
import multiprocessing
cpu_count = multiprocessing.cpu_count()
except (ImportError, NotImplementedError):
pass
prl_exec = "mpirun"
prl_n = "-n"
prl_h = ""
if len(hostfile) > 0:
prl_h += " --hostfile " + hostfile + " "
if cpu_count != 0:
prl_np = cpu_count + nsteerer
else:
prl_np = 4
if nprocesses != 0:
prl_np = nprocesses + nsteerer
#
engine = "qrhei"
if m.log_to_file:
engine += " -lf " + m.log_file_name
engine += " -y " + str(m.verbosity) + "," + str(
m.fverbosity) + " run -q "
# running MPI with proper parallel configuration
prl_cmd = prl_exec + " " + prl_n + " " + str(prl_np) + " " + prl_h
cmd = prl_cmd + engine + scr
if not flag_silent:
qr.printlog("System reports", cpu_count, "processors")
qr.printlog("Starting parallel execution with", prl_np,
"processes (executing command below)")
qr.printlog(">>>", cmd)
qr.printlog("")
try:
p = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
if not flag_silent and (not flag_quiet):
qr.printlog(" --- output below ---\n",
verbose=True,
loglevel=1)
# read and print output
for line in iter(p.stdout.readline, b''):
#for line in p.stdout.readlines():
ln = line.decode()
# line is returned with a \n character at the end
# ln = ln[0:len(ln)-2]
print(ln, end="", flush=True)
retval = p.wait()
except SystemExit:
qr.printlog("", verbose=True, loglevel=qr.LOG_DETAIL)
qr.printlog(" --- Exited by SystemExit --- ",
verbose=True,
loglevel=qr.LOG_DETAIL)
pass
else:
if not flag_silent and (not flag_quiet):
qr.printlog(" --- output below ---\n",
verbose=True,
loglevel=qr.LOG_URGENT)
# running the script within the same interpreter
try:
# launch this properly, so that it gives information
# on the origin of exceptions
with open(scr, 'U') as fp:
code = fp.read()
exec(compile(code, scr, "exec"), globals())
except SystemExit:
qr.printlog("", verbose=True, loglevel=qr.LOG_DETAIL)
qr.printlog(" --- Exited by SystemExit --- ",
verbose=True,
loglevel=qr.LOG_DETAIL)
except:
print(traceback.format_exc())
retval = 0
#
# Saying good bye
#
if retval == 0:
if not flag_silent and (not flag_quiet):
qr.printlog("", verbose=True, loglevel=1)
qr.printlog(" --- output above --- \n",
verbose=True,
loglevel=qr.LOG_URGENT)
qr.printlog("Finished sucessfully; exit code: ",
retval,
verbose=True,
loglevel=1)
else:
qr.printlog("Warning, exit code: ",
retval,
verbose=True,
loglevel=qr.LOG_URGENT)
import numpy
import quantarhei as qr
from quantarhei.utils.vectors import X
import quantarhei.functions as func
from quantarhei.core.units import kB_int
from quantarhei import printlog as print
print("\n***** Rc Simulation Script" + " *****")
input_file = "ex_853_RC.yaml"
INP = qr.Input(input_file, show_input=False) #,
#math_allowed_in =["E0",
# ["params", ["HR", "omega", "rate"]] ])
make_movie = INP.make_movie
show_plots = INP.show_plots
save_containers = INP.save_containers
detailed_balance = INP.detailed_balance
def init_containers():
"""Initialized containers
"""
cont_p_re = qr.TwoDSpectrumContainer()
import shutil
import gc
import numpy
import quantarhei as qr
from quantarhei.utils.vectors import X
import quantarhei.functions as func
from quantarhei.core.units import kB_int
print("\n***** Calculation of material for disorder integration (dimer version) *****")
input_file = "ex_853_RC.yaml"
#input_file = {'E0': 10000.0, 'resonance_coupling': 100.0, 'no_g_vib': 2, 'no_e_vib': 2, 'params': {'HR': 0.01, 'omega': 500.0, 'use_vib': True}, 'location_of_vibrations': 'up', 'append_to_dirname': '_center=600_FWHM=100', 'dip1': [1.5, 0.0, 0.0], 'dip2': [-1.0, -1.0, 0.0], 'rate': '1.0/500.0', 'temperature': 77.0, 't2_N_steps': 100, 't2_time_step': 10.0, 'fine_splitting': 10, 't1_N_steps': 100, 't1_time_step': 10.0, 't3_N_steps': 100, 't3_time_step': 10.0, 'feature_width': 100.0, 'trim_maps_to': [9900, 11500, 9000, 11500], 'omega_uncertainty': 200.0, 'tukey_window_r': 0.3, 'center': 600.0, 'step': 2.0, 'max_available_fwhm': 100.0, 'how_many_fwhm': 2, 'make_movie': False, 'show_plots': False, 'save_containers': False, 'detailed_balance': True, 't2_save_pathways': [50.0, 100.0, 200.0, 300.0], 'copy_input_file_to_results': True, '_math_allowed_in': ['E0', 'resonance_coupling', 'rate', ['params', ['HR', 'omega', 'rate']], 'center', 'step', 'max_available_fwhm', 'how_many_fwhm', 't2_save_pathways']}
INP = qr.Input(input_file, show_input=True) #,
#math_allowed_in =["E0",
# ["params", ["HR", "omega", "rate"]] ])
make_movie = INP.make_movie
show_plots = INP.show_plots
save_containers = INP.save_containers
detailed_balance = INP.detailed_balance
def run(omega, HR, dE, JJ, rate, E0, vib_loc="up", use_vib=True,
stype=qr.signal_REPH, make_movie=False, save_eUt=False,
t2_save_pathways=[], dname=None, trimer=None):
"""Runs a complete set of simulations for a single set of parameters
This example assumes 2D spectra of a dimer with a range of energy gaps
to be precalculated in a designated directory ("sim_up" by default)
"""
import os
import numpy
import quantarhei as qr
INP = qr.Input("ex_854_2DSpectrum_DimerDisorder.yaml")
#math_allowed_in=["E1", "E2", "width_dis"])
if INP.input_file_from_results:
ifile = os.path.join(INP.dname, INP.input_file)
else:
ifile = INP.input_file
INP_pre = qr.Input(ifile, math_allowed_in=INP.with_math_allowed_in)
# directory with the precalculated results
dname = INP.dname #"sim_up"
#
# Transition energy for which the spectra are calculated
#
# # ############################################################################### # # Script initialization # ############################################################################### # # import quantarhei as qr # # Read QTask input file # INP = qr.Input() # # ############################################################################### # # End of initialization # ############################################################################### # #